Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017167.1 Corchorus olitorius cultivar O-4 contig17200, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:495 original size:20 final size:20
Alignment explanation
Indices: 472--515 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
462 TGATTTAAAT
472 TTATATAAAT-TATAATTATA
1 TTATATAAATATATAATTA-A
*
492 TTAT-TATATATATAATTAA
1 TTATATAAATATATAATTAA
511 TTATA
1 TTATA
516 AAACAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATATAAATATATAATTAA
Found at i:1886 original size:86 final size:86
Alignment explanation
Indices: 1741--1912 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
1731 TCCTGTGCGT
1741 TTGTAATCTCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAGAAAAAATTAAAGGTTA
1 TTGTAATCTCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAGAAAAAATTAAAGGTTA
1806 GGCAGCTAACAGCAGCCATGA
66 GGCAGCTAACAGCAGCCATGA
1827 TTGTAATCTCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAGAAAAAATTAAAGGTTA
1 TTGTAATCTCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAGAAAAAATTAAAGGTTA
1892 GGCAGCTAACAGCAGCCATGA
66 GGCAGCTAACAGCAGCCATGA
1913 AAAGAGCTGC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (86 bp):
TTGTAATCTCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAGAAAAAATTAAAGGTTA
GGCAGCTAACAGCAGCCATGA
Found at i:7315 original size:70 final size:70
Alignment explanation
Indices: 7234--7370 Score: 240
Period size: 70 Copynumber: 2.0 Consensus size: 70
7224 AAACGATAGT
* *
7234 GAAACAGTCAAACGA-TGATGAAAGGGTTACAGATAATAATTCGAGTGAAGAAGAGGGCGCTCTC
1 GAAACAATCAAACGATTG-TGAAAGGATTACAGATAATAATTCGAGTGAAGAAGAGGGCGCTCTC
7298 AAAAAC
65 AAAAAC
7304 GAAACAATCAAACGATTGTGAAAGGATTACAGATAATAATTCGAGTGAAGAAGAGGGCGCTCTCA
1 GAAACAATCAAACGATTGTGAAAGGATTACAGATAATAATTCGAGTGAAGAAGAGGGCGCTCTCA
7369 AA
66 AA
7371 TGTCAAAGCC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 62 0.97
71 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (70 bp):
GAAACAATCAAACGATTGTGAAAGGATTACAGATAATAATTCGAGTGAAGAAGAGGGCGCTCTCA
AAAAC
Found at i:12352 original size:31 final size:32
Alignment explanation
Indices: 12289--12360 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
12279 GCCTATGTGT
*
12289 ATAAATTTTAGAAACTCACCCTTAAACCCTCA
1 ATAAATTTCAGAAACTCACCCTTAAACCCTCA
* *
12321 ATAAATTTCAGAAACTCACTCTT-GACCCTCA
1 ATAAATTTCAGAAACTCACCCTTAAACCCTCA
*
12352 A-AAGTTTCA
1 ATAAATTTCA
12361 AGCTAGCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 7 0.19
31 8 0.22
32 21 0.58
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (32 bp):
ATAAATTTCAGAAACTCACCCTTAAACCCTCA
Found at i:20890 original size:12 final size:12
Alignment explanation
Indices: 20873--20916 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
20863 CTTTTTATTA
20873 AAAAAT-ATTTT
1 AAAAATAATTTT
20884 CAAAAATAATTTTT
1 -AAAAATAA-TTTT
20898 AAAAATAATTTT
1 AAAAATAATTTT
*
20910 GAAAATA
1 AAAAATA
20917 TTATTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 16 0.55
13 9 0.31
14 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
AAAAATAATTTT
Found at i:20897 original size:14 final size:13
Alignment explanation
Indices: 20873--20924 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
20863 CTTTTTATTA
*
20873 AAAAAT-ATTTTC
1 AAAAATAATTTTT
20885 AAAAATAATTTTT
1 AAAAATAATTTTT
*
20898 AAAAATAATTTTG
1 AAAAATAATTTTT
*
20911 AAAATATTATTTTT
1 AAAA-ATAATTTTT
20925 GAACTTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 6 0.18
13 21 0.62
14 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:21149 original size:5 final size:5
Alignment explanation
Indices: 21139--21178 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
21129 GAAAAAAGAG
21139 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
21179 TTTCTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:23332 original size:26 final size:26
Alignment explanation
Indices: 23295--23344 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
23285 GTACGCCCGT
*
23295 TGGTAGATTCACCCACCAAAATCAGG
1 TGGTAGACTCACCCACCAAAATCAGG
*
23321 TGGTAGACTCACTCACCAAAATCA
1 TGGTAGACTCACCCACCAAAATCA
23345 CCACTCAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (26 bp):
TGGTAGACTCACCCACCAAAATCAGG
Found at i:23351 original size:16 final size:16
Alignment explanation
Indices: 23330--23360 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23320 GTGGTAGACT
23330 CACTCACCAAAATCAC
1 CACTCACCAAAATCAC
*
23346 CACTCAGCAAAATCA
1 CACTCACCAAAATCA
23361 GGTGGTGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.39, G:0.03, T:0.13
Consensus pattern (16 bp):
CACTCACCAAAATCAC
Found at i:24386 original size:10 final size:10
Alignment explanation
Indices: 24371--24396 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
24361 TATTTCCGTC
24371 AAAAAAGAAA
1 AAAAAAGAAA
24381 AAAAAAGAAA
1 AAAAAAGAAA
24391 AAAAAA
1 AAAAAA
24397 AAAGAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:24396 original size:13 final size:13
Alignment explanation
Indices: 24378--24403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24368 GTCAAAAAAG
24378 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
24391 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
24404 TTCAAGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:44774 original size:26 final size:26
Alignment explanation
Indices: 44745--44798 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
44735 AAATAAATAA
44745 TAAACAAATAAACTAAACTCACATTC
1 TAAACAAATAAACTAAACTCACATTC
44771 TAAACAAATAAACTAAACTCACATTC
1 TAAACAAATAAACTAAACTCACATTC
44797 TA
1 TA
44799 TGAGAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (26 bp):
TAAACAAATAAACTAAACTCACATTC
Found at i:44818 original size:14 final size:14
Alignment explanation
Indices: 44799--44825 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44789 TCACATTCTA
44799 TGAGAATTGAACCG
1 TGAGAATTGAACCG
44813 TGAGAATTGAACC
1 TGAGAATTGAACC
44826 AGAACTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (14 bp):
TGAGAATTGAACCG
Found at i:49697 original size:15 final size:15
Alignment explanation
Indices: 49677--49705 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49667 ACAATTAAGA
49677 CAAATTGTATGATGC
1 CAAATTGTATGATGC
49692 CAAATTGTATGATG
1 CAAATTGTATGATG
49706 ACAACAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (15 bp):
CAAATTGTATGATGC
Found at i:51055 original size:15 final size:16
Alignment explanation
Indices: 51035--51064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51025 TTAATAAAGG
51035 AAAG-AAAAAAGGGGT
1 AAAGAAAAAAAGGGGT
51050 AAAGAAAAAAAGGGG
1 AAAGAAAAAAAGGGG
51065 GAAAATGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAAGGGGT
Found at i:51475 original size:64 final size:64
Alignment explanation
Indices: 51396--51774 Score: 724
Period size: 64 Copynumber: 5.9 Consensus size: 64
51386 TTTGTTGGGG
*
51396 AAGGGGTTTGTTGGCTCATAGATTAACATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
1 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
51460 AA-GGGTTTGTGTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
1 AAGGGGTTTGT-TGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
51524 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
1 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
51588 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
1 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
51652 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
1 AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
51716 AAGGGGTTTGTGTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGT
1 AAGGGGTTTGT-TGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGT
51775 TCTAGCGGTG
Statistics
Matches: 311, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
63 8 0.03
64 248 0.80
65 55 0.18
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (64 bp):
AAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAATCATGTAGCGGTGTACGA
Found at i:74024 original size:11 final size:11
Alignment explanation
Indices: 74000--74051 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
73990 TTGACAACGC
74000 AACAAAAACAA
1 AACAAAAACAA
* *
74011 AACGAAAACGA
1 AACAAAAACAA
74022 AACAAAAACAA
1 AACAAAAACAA
*
74033 AA-AACAGA-AA
1 AACAA-AAACAA
74043 AACAAAAAC
1 AACAAAAAC
74052 GATGCTAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:74681 original size:31 final size:31
Alignment explanation
Indices: 74644--74812 Score: 178
Period size: 31 Copynumber: 5.4 Consensus size: 31
74634 ACGGTGTCCG
* *
74644 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
* * *
74675 ATGTGGCATGCCACGTGTACCAACAAGTGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
**
74706 ACGTATCATGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
* ** **
74737 ACGTGACATGTTATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
* * *
74768 -CTGTGGCATGCCGTGTGTTTCAAAAAAGTGAC
1 AC-GTGGCATGCCATGTG-TACCAAAAAGTGAC
74800 ACGTGGCATGCCA
1 ACGTGGCATGCCA
74813 ATTGCCACGT
Statistics
Matches: 114, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
30 1 0.01
31 90 0.79
32 22 0.19
33 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (31 bp):
ACGTGGCATGCCATGTGTACCAAAAAGTGAC
Found at i:84583 original size:41 final size:41
Alignment explanation
Indices: 84521--84600 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
84511 TTTGACCCTC
* *
84521 CTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCCAT
1 CTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCAT
*
84562 CTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
84601 CTAGATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (41 bp):
CTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCAT
Done.